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- PDB-3u97: 1.1 Angstrom-resolution crystal structure of the Brucella abortus... -

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Basic information

Entry
Database: PDB / ID: 3u97
Title1.1 Angstrom-resolution crystal structure of the Brucella abortus ribonuclease toxin, BrnT
ComponentsRibonuclease toxin BrnT
KeywordsHYDROLASE / RNAse Sa/RelE small ribonuclease fold / ribonuclease / BrnA
Function / homologyRibonuclease toxin, BrnT, of type II toxin-antitoxin system / Ribonuclease toxin, BrnT, of type II toxin-antitoxin system / Ribonuclease toxin BrnT superfamily / Ribonuclease toxin, BrnT, of type II toxin-antitoxin system / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta / BrnT family toxin
Function and homology information
Biological speciesBrucella abortus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.102 Å
AuthorsHeaton, B. / Herrou, J. / Crosson, S.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Molecular Structure and Function of the Novel BrnT/BrnA Toxin-Antitoxin System of Brucella abortus.
Authors: Heaton, B.E. / Herrou, J. / Blackwell, A.E. / Wysocki, V.H. / Crosson, S.
History
DepositionOct 18, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 7, 2012Group: Database references
Revision 1.2Apr 25, 2012Group: Database references
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ribonuclease toxin BrnT


Theoretical massNumber of molelcules
Total (without water)13,1551
Polymers13,1551
Non-polymers00
Water1,54986
1
A: Ribonuclease toxin BrnT

A: Ribonuclease toxin BrnT

A: Ribonuclease toxin BrnT

A: Ribonuclease toxin BrnT


Theoretical massNumber of molelcules
Total (without water)52,6194
Polymers52,6194
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
Buried area6460 Å2
ΔGint-47 kcal/mol
Surface area13820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.420, 74.420, 29.607
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4
Components on special symmetry positions
IDModelComponents
11A-126-

HOH

21A-134-

HOH

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Components

#1: Protein Ribonuclease toxin BrnT


Mass: 13154.646 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella abortus (bacteria) / Strain: 9-941 / Gene: BruAb1_0981 / Plasmid: pET151 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Rosetta(DE3)/pLysS / References: UniProt: Q57DF0, EC: 3.1.27.1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.56 Å3/Da / Density % sol: 21.06 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 100 mM Tris buffer, 8% PEG 6000, 150 mM NaCl, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 287K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.02 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 24, 2011
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.02 Å / Relative weight: 1
ReflectionResolution: 1.1→22.121 Å / Num. all: 33026 / Num. obs: 31054 / % possible obs: 94 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.1→1.1291 Å / % possible all: 94

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
SOLVEphasing
PHENIX(phenix.refine: 1.7.2_869)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.102→22 Å / SU ML: 0.24 / σ(F): 0 / Phase error: 12.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1577 1906 6.14 %random
Rwork0.1396 ---
all0.1407 33026 --
obs0.1407 31054 94.03 %-
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.932 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.8669 Å2-0 Å20 Å2
2---0.8669 Å2-0 Å2
3---1.7339 Å2
Refinement stepCycle: LAST / Resolution: 1.102→22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms606 0 0 86 692
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016688
X-RAY DIFFRACTIONf_angle_d1.674943
X-RAY DIFFRACTIONf_dihedral_angle_d12.105273
X-RAY DIFFRACTIONf_chiral_restr0.121108
X-RAY DIFFRACTIONf_plane_restr0.009121
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.102-1.12910.30491060.31721595X-RAY DIFFRACTION72
1.1291-1.15960.29811170.23641865X-RAY DIFFRACTION85
1.1596-1.19370.20451260.18881965X-RAY DIFFRACTION89
1.1937-1.23230.18221360.14912050X-RAY DIFFRACTION93
1.2323-1.27630.15381350.13332029X-RAY DIFFRACTION94
1.2763-1.32740.1511380.11072090X-RAY DIFFRACTION95
1.3274-1.38780.12441330.10682086X-RAY DIFFRACTION95
1.3878-1.46090.13221380.10622171X-RAY DIFFRACTION97
1.4609-1.55250.13821450.09962160X-RAY DIFFRACTION98
1.5525-1.67230.121390.10392173X-RAY DIFFRACTION99
1.6723-1.84050.12211460.10852204X-RAY DIFFRACTION99
1.8405-2.10660.13451480.11872242X-RAY DIFFRACTION100
2.1066-2.65340.15431440.1282232X-RAY DIFFRACTION100
2.6534-22.12530.17611550.16882286X-RAY DIFFRACTION100

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